Cilia and flagella are eukaryotic organelles essential for both motility and sensory transduction in animals, animals and protozoa. These organelles share a long rod-shaped microtubular axoneme that projects away from the cell body for long distances ranging from 5 to 100 mum or more. Assembly of these organelles is an engineering problem for the cell, because assembly occurs at the distal end of the organelle, many microns away from the cell body. This problem is solved by a mechanism called Intraflagellar Transport (IFT), which involves the bidirectional movement of molecular rafts along the long axis of these organelles. IFT was first identified in the biflagellate green alga, Chlamydomonas, the model organism for the study of IFT. More recently, IFT has been shown to occur in animals and is now thought to function in most, if not all, ciliated cells. In Chlamydomonas, IFT rafts are ferried upstream to the flagellar tip by FLA10 kinesin-II and downstream to the cell body by cytoplasmic dynein 1B. A primary function of this transport is thought to be delivery of a cargo of axonemal precursors upstream to the site of axonemal assembly. It has also been hypothesized that IFT functions to ferry signals downstream from the tips of cilia and flagella to the cell body, thereby mediating the signal transduction of external stimuli. This transfer of IFT cargo must involve the interaction of IFT raft proteins with flagellar structural proteins. Consistent with this hypothesis, we have found that each of three IFT raft proteins, p57, p88 and p172, contain different repetitive amino acid sequences. Two of these, the coiled-coil motif of p57 and the tetratricopeptide repeat (TPR) of p88 are well known as protein-protein interaction domains. To understand the biological function of these three subunits, we will (1) identify mutants with disruptions of these three IFT genes, and, (2) identify proteins that associate directly with these three IFT raft subunits. These studies will allow us to understand how IFT particles transfer their cargo during the assembly and function of eukaryotic cilia and flagella at the molecular level. The results of these studies may lead to effective treatments for ciliary-dependent diseases, including Kartagener's Syndrome.